Personalized bacteriophage therapy to treat pandrug-resistant spinal Pseudomonas aeruginosa infection

Bone and joint infections (BJI) are one of the most difficult-to-treat bacterial infection, especially in the era of antimicrobial resistance. Lytic bacteriophages (phages for short) are natural viruses that can selectively target and kill bacteria. They are considered to have a high therapeutic potential for the treatment of severe bacterial infections and especially BJI, as they also target biofilms. Here we report on the management of a patient with a pandrug-resistant Pseudomonas aeruginosa spinal abscess who was treated with surgery and a personalized combination of phage therapy that was added to antibiotics. As the infecting P. aeruginosa strain was resistant to the phages developed by private companies that were contacted, we set up a unique European academic collaboration to find, produce and administer a personalized phage cocktail to the patient in due time. After two surgeries, despite bacterial persistence with expression of small colony variants, the patient healed with local and intravenous injections of purified phages as adjuvant therapy.

This is a well-done and interesting case report of a challenging case of a patient with pan-resistant Pseudomonas spinal infection. There are several noteworthy results which contributes to the field and demonstrates the complexities and nuances of the role of phage therapy in very challenging cases.
Several notable aspects of this case: 1-Combination of direct administration and systemic phages 2-Done in conjunction with aggressive staged surgical approach 3-Done in conjunction with standard of care antibiotics 4-Highly personalized with evolving plan tailored to the clinical case 5-Demonstrates collaborative effort to newly source a phage One issue for this case is lack of proof that the phages provided added benefit to the conventional practice of staged surgical approach in conjunction with antibiotics, which the authors acknowledge. This same issue applies to any treatment which is adjunctive. However, I wonder if that authors can provide any perspective on how a patient with spinal hardware implanted in the presence of positive P. aeruginosa cultures can be expected to perform? Can expected success or failure rates be estimated based on historical data to act as a control?
Other clarifications the authors can provide: 1-Was there quantification of the bacterial growth at the time of the 2 surgeries? (1+, 2+, etc?).
2-How was the timing of the second stage determined? Was it based on clinical signs, symptoms and imaging or decided a priori?
3-Did the authors use any particular indicators to help determine the duration of phage and antibiotic treatments? 4-Were there any "before" clinical photos that can be provided for comparison to Panel O?
Minor comments: Line 15: "2-stage approach" typically refers to specifically to a "2-stage exchange" in the musculoskeletal infection literature, wherein infected hardware is removed and exchanged for new hardware in a staged fashion. I would use the term "staged approach" instead.
Line 17: Add "was" cured Line 34-38: Was the initial P. aeruginosa isolate susceptible to meropenem and colistin? If not, was there an attempt to document successful clearance of the bacteremia?
Line 41: Use "aspiration" instead of puncture Line 57: Use "In collaboration, we" instead of "We collegially" Line 60 and throughout manuscript: Use "disc" instead of "discal" Line 66: Remove "extemporaneously" and use "in real time" Line 72: "over" 3 hours Line 77: Use "concentration" instead of "dilution" Line 98-99: use "no phages are commercially available" instead of "on the market" Line 100-101: Sentence with "Few data…." Is this true? There are many case reports on phages in BJI.
Line 204: What is meant by "mirror-like" here?
Line 224: Correct the spelling of lumbar Reviewer #2 (Remarks to the Author): 1.The authors claim (line 100) that: "few data have been published about phage therapy in patients with BJI". However, four reviews on that subject appeared just in the recent months: 1. Genevieve J et al EFORT Open Rev 2021,10,11482.Ferry T et al Viruses 2021,13,24143.van Nieuwenhuyse B et al Viruses 2021,13,18984.Walter N et al Orthopede 2022,51138. Does this report provide any important new information that would justify its presentation to to acientific and medical community? This reviewer finds it difficult to agree on that.
2.line 45: "the patient developed acute kidney injury and the antibiotics were rapidly stopped". This condition (also referred to as acute renal failure) is a medical emergency usually requiring dialysis. However, there is no comment on how this grave complication was treated. If indeed hemodialysis was applied then some discussion on its possible influence on phage therapy should be added.
Yes, and the results do not provide evidence for the effectiveness of phage therapy -shouldn't that fact be mentioned? 4.line 95: "the patient died of COVID" -if the authors believe that their report provides support for clinical application of phage therapy then some discussion to exclude phage contribution to the patient's death should be added. 5.line 112: "European academic collaboration is crucial to develop the field". Of course, but a clear statement that such collaboration should primarily involve clinical trials is lacking. "Response to referees" letter above the manuscript NCOMMS-22-01270-T

Reviewer #1 (Remarks to the Author):
This is a well-done and interesting case report of a challenging case of a patient with panresistant Pseudomonas spinal infection. There are several noteworthy results which contributes to the field and demonstrates the complexities and nuances of the role of phage therapy in very challenging cases.
Several notable aspects of this case: 1-Combination of direct administration and systemic phages 2-Done in conjunction with aggressive staged surgical approach 3-Done in conjunction with standard of care antibiotics 4-Highly personalized with evolving plan tailored to the clinical case 5-Demonstrates collaborative effort to newly source a phage Answer: Thanks for these comments.
One issue for this case is lack of proof that the phages provided added benefit to the conventional practice of staged surgical approach in conjunction with antibiotics, which the authors acknowledge. This same issue applies to any treatment which is adjunctive. However, I wonder if that authors can provide any perspective on how a patient with spinal hardware implanted in the presence of positive P. aeruginosa cultures can be expected to perform? Can expected success or failure rates be estimated based on historical data to act as a control?
Answer: Thanks for this comment. This is an important question. There is no data about the risk of failure in patients with P. aeruginosa persistent spinal infection at the time of reconstruction, especially as P. aeruginosa is not a common pathogen in this setting, and as patients who need reconstruction are only part of the patients who experienced spondylodiscitis. However, there are some data that indicating that the risk of failure is probably high in our patient. First, positive culture at the time of reconstruction has to be considered as an implant-associated infection, for which the use of drugs that have antibiofilm activity is crucial to improve the prognosis. Fluoroquinolone is a family of antibiotics that is considered to have anti-biofilm activity against Gram-negative bacteria. In the paper published by Köder et al. in 2020 in the journal "Infection", the authors reported that patients with spinal implant-associated infections treated without biofilmactive antibiotics was associated with a worse outcome, and with a higher post-operative pain intensity in comparison with patients treated with biofilm-active antibiotics. Of note, few patients were infected with Gram-negative bacteria in this study, none of them were infected with P. aeruginosa, and all Gram-negative bacteria were associated with polymicrobial infection. Despite the limitation of the interpretation of the results in this study dedicated to spinal implant-infection, our group published concordant results in a retrospective cohort study that has been performed in patients with implant-associated P.

aeruginosa infection (Cerioli et al. Frontiers Medicine 2020). Among the 90 patients included in the study, 15 had spinal implant associated infection due to P. aeruginosa.
This study indicated that the use of fluoroquinolone influenced the prognosis, with a cumulative probability of failure of 90% for patients for whom a fluoroquinolone was not prescribed (mainly due to antimicrobial resistance) ( Figure 1C). In the case presented here, no fluoroquinolone was used, as the strain responsible for the infection was a multidrug resistant strain. We added in the discussion section of the manuscript the following sentence: "Indeed, without the use of antibiotics that have anti-biofilm activity (i.e. rifampin in staphylococcal implant-associated infections, or a fluoroquinolone in Gramnegative infections), the cumulative probability of failure is considered as very high in patients with implant-associated infections. In the case presented here, a fluoroquinolone was not usable due to the multidrug resistance profile of the strain, and the anti-biofilm activity of the phages that have been used to treat the patient potentially helps for the cure." We added the references Köder et al. and Cerioli et al.
Other clarifications the authors can provide: 1-Was there quantification of the bacterial growth at the time of the 2 surgeries? (1+, 2+, etc?).
Answer: Bacterial quantification was not mentioned in the manuscript because analytical procedures for bone samples are not standardized to provide reliable quantification of bacteria (important variations of the sample size which is diluted in sterile water for grinding, homogenization is often difficult etc.). However, the number of positive samples out of the total number of samples taken during the surgery is more interesting. Indeed, 6/7 samples taken during the first surgery were positive versus 2/6 samples taken during the second surgery. We added these informations in the manuscript.
2-How was the timing of the second stage determined? Was it based on clinical signs, symptoms and imaging or decided a priori?
Answer: Thanks for this question. The timing of the second stage is mainly based on our experience, so decided a priori. It is usual to perform the second stage after an antibiotic window of at least two weeks. Of course, in case of clinical signs of relapse during the initial antimibrobial therapy or during the antibiotic window, a new debridement has to be done, and the reconstruction has to be delayed.

3-Did the authors use any particular indicators to help determine the duration of phage and antibiotic treatments?
Answer: Thanks for this comment. We are using the data from the literature and different guidelines to determine the duration of antimicrobial therapy. In patients with a native hematogenous spinal infection, a duration of 6 weeks is usual. In patients with an implantassociated infection, the usual duration is frequently 3 months. Some patients with persistent infection at the time of reconstruction could be qualified for undefinite suppressive antimicrobial treatment (i.e. a life-long daily intake of antibiotics), that was not possible in the case presented here, as no oral options were available.